Due to a problem in the Quartus® II software, you might see this error when you use the PCIe Hard IP (HIP) with a virtual pin assignment for the signal PERSTN. This error may be accompanied by the following messages:
Internal Error: Sub-system: ASM, File: /quartus/comp/asm/asm_le.cpp, Line: 4890
ERROR: The illegal route at re_dest_type=1424 with atom_type=STRATIXV_HSSI_GEN3_PCIE_HIP, atom_id=98888 and atom_iterm=I_PINPERSTN, from atom STRATIXV_LCELL_COMB of id=212229
This error occurs because an LCELL is inserted on PERSTN for the virtual pin assignment.
To avoid this error, remove the virtual pin assignment from Quartus II settings file (.qsf) and edit the source code to remove the input pin.
This problem is fixed in the Quartus® II software v12.0.